*Target (protein/gene name):Tyrosine-protein phosphatase YwqE *NCBI Gene # or RefSeq#: 452913202 *Protein ID (NP or XP #) or Wolbachia#: ZP_21961830.1 *Organism (including strain): bacillus subtilis Etiologic Risk Group (see link below): Risk Group 1 (RG1) Agents *Background/Disease Information:
Protein-tyrosine phosphatases, PTP, exist as large protein families and play a critical role in regulating cellular signal transduction, cell transformation and metabolism. In addition, PTP controls tyrosine phosphorylation and dephosphorylation, which plays an important role during many processes of the immune system. Thus, many evidence has shown that PTPs can suppress tumors since, in cancer, oncogenic activation of tyrosine kinases is a common feature, and original anticancer drugs have been introduced that can target these enzymes [1]. Since protein tyrosine kinases (PTK) and PTP work antagonistically to regulate cellular signal transduction and to determine the condition of tyrosine phosphorylation in a protein, it is crucial to state the specific activities of PTKs and PTPs [2]. Furthermore, sustaining a steady level of protein tyrosine phosphorylation is critical for cellular functions because it creates recognitions for protein interactions as well as controls enzyme activity.
Figure 1: PyMol image of protein 3QY6 shown in ribbons.
http://www.rcsb.org/pdb/images/3qy6_bio_r_500.jpg *Amino Acid Sequence (paste as text only - not as screenshot or as 'code'):
MIDIHCHILPAMDDGAGDSADSIEMARAAVRQGIRTIIATPHHNNGVYKNEPAAVREAADQLNKRLIKEDIPLHVLPGQE
IRIYGEVEQDLAKRQLLSLNDTKYILIEFPFDHVPRYAEQLFYDLQLKGYIPVIAHPERNREIRENPSLLYHLVEKGAAS
QITSGSLAGIFGKQLKAFSLRLVEANLIHFVASDAHNVKTRNFHTQEALYVLEKEFGSELPYMLTENAELLLRNQTIFRQ
PPQPVKRRKLFGFFLEHHHHHH *length of your protein in Amino Acids: 262 Molecular Weight of your protein in kiloDaltons using the Expasy ProtParamwebsite: 30023.3 kD Molar Extinction coefficient of your protein at 280 nm wavelength: 13410 http://web.expasy.org/cgi-bin/protparam/protparam TMpred graph Image (http://www.ch.embnet.org/software/TMPRED_form.html). Input your amino acid sequence to it. *CDS Gene Sequence (paste as text only): ATGATCGATATTCACTGTCACATTCTTCCCGCAATGGATGACGGGGCAGGTGATTCGGCCGACAGCATAG AAATGGCAAGAGCAGCTGTTCGTCAGGGAATCCGGACGATCATTGCGACACCTCATCATAACAACGGTGT GTATAAAAACGAGCCAGCCGCAGTCAGAGAAGCAGCAGATCAGTTAAACAAACGTTTAATCAAAGAAGAC ATTCCTTTACATGTGCTTCCGGGACAGGAAATCAGAATCTACGGCGAGGTGGAACAAGACCTTGCCAAAC AGCAGCTGCTTTCGCTGAATGATACAAAACACATCTTGATTGAGTTTCCGTTTGATCACGTTCCCCGATA TGCGGAGCAGCTTTTTTATGATTTGCAGCTGAAAGGATATATTCCGGTTATCGCCCATCCTGAACGCAAC AGGGAAATTCGCGAAAACCCGTCTTTGCTGTATCATCTTGTGGAAAAAGGAGCAGCATCTCAGATTACTT CAGGAAGTCTTGCGGGGACCTTCGGCAAGCAGCTGAAAGCATTTTCTCTCCGGCTGGTTGAAGCCAATTT GATCCATTTCGTAGCCTCAGATGCCCATAATGTGAAAACGAGAAATTTTCACACTCAAGAGGCTCTTTAT GTTCTAGAGAAAGAATTCGGCTCGGAACTTCCTTATATGCTGACGGAAAATGCAGAGCTTCTCCTGCGGA ATCAGACCATCTTCAGACAGCCTCCGCAACCGGTCAAAAGAAGAAAATTGTTTGGTCTTTTTTAA *GC% Content for gene: 45.75% *CDS Gene Sequence (codon optimized) - copy from output of Primer Design Protocol (paste as text only):
ATGATTGATATTCATTGTCACATCCTTCCGGCTATGGACGATGGTGCAGGTGATTCAGCGGATAGCATTGAAATGGCGCGGGCGGCTGTA
CGCCAAGGTATCCGTACTATTATCGCTACACCTCATCACAATAATGGAGTCTACAAAAATGAGCCAGCAGCCGTTCGTGAAGCAGCGGAC CAACTCAATAAGCGGCTGATAAAAGAAGACATCCCGCTTCATGTCTTACCTGGCCAAGAAATCCGGATTTACGGGGAGGTAGAACAGGAT TTGGCAAAACAACAATTATTAAGCCTGAATGACACGAAGCACATCTTGATTGAGTTTCCTTTCGATCATGTGCCGCGTTACGCGGAGCAA TTATTTTATGATCTTCAGTTAAAAGGTTATATTCCGGTGATCGCCCATCCGGAGAGAAATCGCGAAATTCGTGAGAATCCATCTTTATTG TATCATTTGGTCGAAAAAGGCGCTGCGTCTCAGATCACCTCAGGCAGCCTTGCTGGAACATTTGGTAAACAACTTAAGGCGTTCTCCTTA CGTTTGGTAGAAGCTAACCTTATCCACTTTGTTGCGAGTGATGCCCATAACGTCAAAACGAGAAACTTTCATACACAGGAAGCGTTATAT GTTTTGGAGAAGGAGTTTGGATCAGAACTTCCGTATATGCTGACCGAAAATGCGGAATTGTTATTAAGAAACCAGACAATCTTTCGTCAA CCACCGCAGCCGGTGAAACGGAGAAAACTTTTTGGACTTTTTTAA *GC% Content for gene (codon optimized): 44.18%
*NCBI Gene # or RefSeq#: 452913202
*Protein ID (NP or XP #) or Wolbachia#: ZP_21961830.1
*Organism (including strain): bacillus subtilis
Etiologic Risk Group (see link below): Risk Group 1 (RG1) Agents
*Background/Disease Information:
Protein-tyrosine phosphatases, PTP, exist as large protein families and play a critical role in regulating cellular signal transduction, cell transformation and metabolism. In addition, PTP controls tyrosine phosphorylation and dephosphorylation, which plays an important role during many processes of the immune system. Thus, many evidence has shown that PTPs can suppress tumors since, in cancer, oncogenic activation of tyrosine kinases is a common feature, and original anticancer drugs have been introduced that can target these enzymes [1]. Since protein tyrosine kinases (PTK) and PTP work antagonistically to regulate cellular signal transduction and to determine the condition of tyrosine phosphorylation in a protein, it is crucial to state the specific activities of PTKs and PTPs [2]. Furthermore, sustaining a steady level of protein tyrosine phosphorylation is critical for cellular functions because it creates recognitions for protein interactions as well as controls enzyme activity.
Essentiality of this protein: Essential
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC14801/
Complex of proteins?: No.
Druggable Target: Yes.
*EC#: 3.1.3.48
Link to BRENDA EC# page:
http://www.brenda-enzymes.org/php/result_flat.php4?ecno=3.1.3.48&Suchword=&organism[]=Bacillus+subtilis&show_tm=0
Enzyme Assay information (spectrophotometric, coupled assay ?, reagents): spectrophotometric
-- link to Sigma (or other company) page for assay or assay reagents (substrates)
http://www.sigmaaldrich.com/catalog/product/sigma/p6244?lang=en®ion=US
-- link (or citation) to paper that contains assay information
http://www.ncbi.nlm.nih.gov/pubmed/15588980
-- List cost and quantity of substrate reagents and supplier
P6244-50UG: $467.50 (≥30 units/mg protein)
Structure Available (PDB or Homology model
-- PDB # or closest PDB entry if using homology model: 3QY7
-- For Homology Model option:
---- Show pairwise alignment of your BLASTP search in NCBI against the PDB
---- Query Coverage: 100%
---- Max % Identities: 254/254 100%
---- % Positives: 254/254 100%
---- Chain used for homology: Chain A
Current Inhibitors: ((1E)-2-nitroprop-1-en-1-yl)benzene
http://www.brenda-enzymes.org/php/result_flat.php4?ecno=3.1.3.48
Expression Information (has it been expressed in bacterial cells): Yes, expressed through E. coli.
Purification Method:
http://www.ncbi.nlm.nih.gov/pubmed/12112018
Image of protein (PyMol with features delineated and shown separately):
http://www.rcsb.org/pdb/images/3qy6_bio_r_500.jpg
*Amino Acid Sequence (paste as text only - not as screenshot or as 'code'):
MIDIHCHILPAMDDGAGDSADSIEMARAAVRQGIRTIIATPHHNNGVYKNEPAAVREAADQLNKRLIKEDIPLHVLPGQE
IRIYGEVEQDLAKRQLLSLNDTKYILIEFPFDHVPRYAEQLFYDLQLKGYIPVIAHPERNREIRENPSLLYHLVEKGAAS
QITSGSLAGIFGKQLKAFSLRLVEANLIHFVASDAHNVKTRNFHTQEALYVLEKEFGSELPYMLTENAELLLRNQTIFRQ
PPQPVKRRKLFGFFLEHHHHHH
*length of your protein in Amino Acids: 262
Molecular Weight of your protein in kiloDaltons using the Expasy ProtParamwebsite: 30023.3 kD
Molar Extinction coefficient of your protein at 280 nm wavelength: 13410
http://web.expasy.org/cgi-bin/protparam/protparam
TMpred graph Image (http://www.ch.embnet.org/software/TMPRED_form.html). Input your amino acid sequence to it.
*CDS Gene Sequence (paste as text only):
ATGATCGATATTCACTGTCACATTCTTCCCGCAATGGATGACGGGGCAGGTGATTCGGCCGACAGCATAG AAATGGCAAGAGCAGCTGTTCGTCAGGGAATCCGGACGATCATTGCGACACCTCATCATAACAACGGTGT GTATAAAAACGAGCCAGCCGCAGTCAGAGAAGCAGCAGATCAGTTAAACAAACGTTTAATCAAAGAAGAC ATTCCTTTACATGTGCTTCCGGGACAGGAAATCAGAATCTACGGCGAGGTGGAACAAGACCTTGCCAAAC AGCAGCTGCTTTCGCTGAATGATACAAAACACATCTTGATTGAGTTTCCGTTTGATCACGTTCCCCGATA TGCGGAGCAGCTTTTTTATGATTTGCAGCTGAAAGGATATATTCCGGTTATCGCCCATCCTGAACGCAAC AGGGAAATTCGCGAAAACCCGTCTTTGCTGTATCATCTTGTGGAAAAAGGAGCAGCATCTCAGATTACTT CAGGAAGTCTTGCGGGGACCTTCGGCAAGCAGCTGAAAGCATTTTCTCTCCGGCTGGTTGAAGCCAATTT GATCCATTTCGTAGCCTCAGATGCCCATAATGTGAAAACGAGAAATTTTCACACTCAAGAGGCTCTTTAT GTTCTAGAGAAAGAATTCGGCTCGGAACTTCCTTATATGCTGACGGAAAATGCAGAGCTTCTCCTGCGGA ATCAGACCATCTTCAGACAGCCTCCGCAACCGGTCAAAAGAAGAAAATTGTTTGGTCTTTTTTAA
*GC% Content for gene: 45.75%
*CDS Gene Sequence (codon optimized) - copy from output of Primer Design Protocol (paste as text only):
ATGATTGATATTCATTGTCACATCCTTCCGGCTATGGACGATGGTGCAGGTGATTCAGCGGATAGCATTGAAATGGCGCGGGCGGCTGTA
CGCCAAGGTATCCGTACTATTATCGCTACACCTCATCACAATAATGGAGTCTACAAAAATGAGCCAGCAGCCGTTCGTGAAGCAGCGGAC CAACTCAATAAGCGGCTGATAAAAGAAGACATCCCGCTTCATGTCTTACCTGGCCAAGAAATCCGGATTTACGGGGAGGTAGAACAGGAT TTGGCAAAACAACAATTATTAAGCCTGAATGACACGAAGCACATCTTGATTGAGTTTCCTTTCGATCATGTGCCGCGTTACGCGGAGCAA TTATTTTATGATCTTCAGTTAAAAGGTTATATTCCGGTGATCGCCCATCCGGAGAGAAATCGCGAAATTCGTGAGAATCCATCTTTATTG TATCATTTGGTCGAAAAAGGCGCTGCGTCTCAGATCACCTCAGGCAGCCTTGCTGGAACATTTGGTAAACAACTTAAGGCGTTCTCCTTA CGTTTGGTAGAAGCTAACCTTATCCACTTTGTTGCGAGTGATGCCCATAACGTCAAAACGAGAAACTTTCATACACAGGAAGCGTTATAT GTTTTGGAGAAGGAGTTTGGATCAGAACTTCCGTATATGCTGACCGAAAATGCGGAATTGTTATTAAGAAACCAGACAATCTTTCGTCAA CCACCGCAGCCGGTGAAACGGAGAAAACTTTTTGGACTTTTTTAA
*GC% Content for gene (codon optimized): 44.18%
Resource Websites:
[1] Ostman, A.; Hellberg. C.; Bohmer, F. D., Protein-tyrosine phosphatases and cancer. Nat Rev Cancer 2006, 6, (4), 307-20.
[2] Lorenz, U., Protein Tyrosin Phosphatase Assays. Curr Protoc Immunol 2011, 11.
http://www.brenda-enzymes.org/php/result_flat.php4?ecno=3.1.3.48&Suchword=&organism[]=Bacillus+subtilis&show_tm=0
http://www.ncbi.nlm.nih.gov/blast/Blast.cgi
http://www.ncbi.nlm.nih.gov/protein/452913202?report=fasta
http://www.rcsb.org/pdb/explore/explore.do?structureId=3QY6
http://web.expasy.org/cgi-bin/protparam/protparam
http://www.ch.embnet.org/cgi-bin/TMPRED_form_parser
http://www.ncbi.nlm.nih.gov/gene/14270982#reference-sequences